Strain identifier
BacDive ID: 3955
Type strain: 
Species: Desulfobacter hydrogenophilus
Strain Designation: AcRS1
Strain history: <- F. Widdel, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; AcRS1 <- F. Widdel {1984}
NCBI tax ID(s): 2291 (species)
version 8.1 (current version)
General
@ref: 1366
BacDive-ID: 3955
DSM-Number: 3380
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Desulfobacter hydrogenophilus AcRS1 is an anaerobe, mesophilic, motile bacterium that was isolated from marine mud.
NCBI tax id
- NCBI tax id: 2291
- Matching level: species
strain history
- @ref: 1366
- history: <- F. Widdel, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; AcRS1 <- F. Widdel {1984}
doi: 10.13145/bacdive3955.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfobacterales
- family: Desulfobacteraceae
- genus: Desulfobacter
- species: Desulfobacter hydrogenophilus
- full scientific name: Desulfobacter hydrogenophilus Widdel 1988
@ref: 1366
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfobacterales
family: Desulfobacteraceae
genus: Desulfobacter
species: Desulfobacter hydrogenophilus
full scientific name: Desulfobacter hydrogenophilus Widdel 1988
strain designation: AcRS1
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 95.589 | |
| 69480 | 99.997 | negative |
Culture and growth conditions
culture medium
- @ref: 1366
- name: DESULFOBACTER MEDIUM (DSMZ Medium 195)
- growth: yes
- link: https://mediadive.dsmz.de/medium/195
- composition: Name: DESULFOBACTER MEDIUM (DSMZ Medium 195) Composition: NaCl 20.9372 g/l Na2SO4 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l Na-acetate x 3 H2O 2.49252 g/l Na2CO3 1.49551 g/l KCl 0.498504 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water
culture temp
- @ref: 1366
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 1366 | anaerobe | |
| 69480 | anaerobe | 99.473 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.821 |
Isolation, sampling and environmental information
isolation
- @ref: 1366
- sample type: marine mud
- geographic location: Venice
- country: Italy
- origin.country: ITA
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Terrestrial | #Mud (Sludge) |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_117936.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_40;96_3037;97_7840;98_63802;99_117936&stattab=map
- Last taxonomy: Desulfobacter hydrogenophilus subclade
- 16S sequence: FR733673
- Sequence Identity:
- Total samples: 6
- aquatic counts: 6
Safety information
risk assessment
- @ref: 1366
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | D.hydrogenophilus 16S ribosomal rRNA | M34412 | 1390 | ena | 2291 |
| 1366 | Desulfobacter hydrogenophilus partial 16S rRNA gene, type strain DSM3380T | FR733673 | 1549 | ena | 2291 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Desulfobacter hydrogenophilus AcRS1 | GCA_004319545 | chromosome | ncbi | 2291 |
| 66792 | Desulfobacter hydrogenophilus DSM 3380 | GCA_003261095 | scaffold | ncbi | 2291 |
| 66792 | Desulfobacter hydrogenophilus DSM 3380 | GCA_010499545 | contig | ncbi | 2291 |
| 66792 | Desulfobacter hydrogenophilus strain DSM 3380 | 2291.7 | wgs | patric | 2291 |
| 66792 | Desulfobacter hydrogenophilus strain DSM 3380 | 2291.4 | wgs | patric | 2291 |
| 66792 | Desulfobacter hydrogenophilus DSM 3380 | 2890690344 | draft | img | 2291 |
GC content
- @ref: 1366
- GC-content: 44.6
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 87.955 | no |
| flagellated | no | 62.956 | no |
| gram-positive | no | 98.637 | no |
| anaerobic | yes | 98.208 | yes |
| aerobic | no | 95.055 | yes |
| halophile | no | 70.556 | no |
| spore-forming | no | 85.391 | no |
| glucose-util | yes | 53.411 | no |
| thermophile | no | 98.986 | yes |
| glucose-ferment | no | 86.479 | no |
External links
@ref: 1366
culture collection no.: DSM 3380, ATCC 43915
straininfo link
- @ref: 73464
- straininfo: 42122
literature
- topic: Genetics
- Pubmed-ID: 32241859
- title: Draft Genome Sequence of Desulfobacter hydrogenophilus DSM 3380, a Psychrotolerant Sulfate-Reducing Bacterium.
- authors: Bertran E, Ward LM, Johnston DT
- journal: Microbiol Resour Announc
- DOI: 10.1128/MRA.00203-20
- year: 2020
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1366 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3380) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3380 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 73464 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42122.1 | StrainInfo: A central database for resolving microbial strain identifiers |